modailty treatment now linked to condition

Author: gkennos

CHANGELOG.md

@@ -129,4 +129,7 @@
 - correcting fraction filter
 
 ## 0.3.17
-- modality treatment join
+- modality treatment join
+
+## 0.3.18
+- modailty treatment now linked to condition

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "omop-constructs"
-version = "0.3.17"
+version = "0.3.18"
 description = "For building complex constructs on top of the omop-alchemy library."
 readme = "README.md"
 authors = [

src/omop_constructs/alchemy/episodes/__init__.py

@@ -7,7 +7,8 @@
 from .fraction_mv import FractionMV
 from .treatment_summary_mv import ConditionTreatmentEpisode
 from .treatment_envelope_mv import TreatmentEnvelopeMV
-from .modality_intent_mv import EpisodeTreatmentMV
+from .modality_intent_mv import TreatmentIntentMV, ConditionTreatmentIntentMV
+
 __all__ = [
     "OverarchingDiseaseEpisodeMV",
     "TreatmentRegimenCycleMV",
@@ -21,5 +22,6 @@
     "FractionMV",
     "ConditionTreatmentEpisode",
     "TreatmentEnvelopeMV",
-    "EpisodeTreatmentMV",
+    "TreatmentIntentMV",
+    "ConditionTreatmentIntentMV",
 ]

src/omop_constructs/alchemy/episodes/modality_intent_join.py

@@ -21,6 +21,7 @@
     .distinct(Episode_Event.episode_id)
     .subquery()
 )
+
 modality_rt = (
     sa.select(
         sa.literal(True).label('rt'),
@@ -39,11 +40,13 @@
     .distinct(Episode_Event.episode_id)
     .subquery()
 )
+
 episode_intent = (
     sa.select(
         Episode.episode_id,
         Episode.episode_start_date,
         Episode.episode_end_date,
+        Episode.episode_parent_id,
         Measurement.measurement_concept_id,
         intent_concept.concept_name,
     )
@@ -55,17 +58,21 @@
         )
     )
     .join(intent_concept, intent_concept.concept_id==Measurement.measurement_concept_id)
+    .filter(
+        Measurement.measurement_concept_id.in_(runtime.treatment_modifiers.treatment_intent.ids)
+    )
     .subquery()
 )
 
 episode_join = (
     sa.select(
         sa.func.row_number().over().label("mv_id"),
-        episode_intent.c.episode_id,
-        episode_intent.c.episode_start_date,
-        episode_intent.c.episode_end_date,
-        episode_intent.c.measurement_concept_id,
-        episode_intent.c.concept_name,
+        episode_intent.c.episode_id.label('treatment_episode_id'),
+        episode_intent.c.episode_start_date.label('treatment_episode_start_date'),
+        episode_intent.c.episode_end_date.label('treatment_episode_end_date'),
+        episode_intent.c.episode_parent_id.label('treatment_episode_parent_id'),
+        episode_intent.c.measurement_concept_id.label('treatment_intent_concept_id'),
+        episode_intent.c.concept_name.label('treatment_intent_name'),
         modality_rt.c.rt,
         modality_sact.c.sact,
         sa.and_(

src/omop_constructs/alchemy/episodes/modality_intent_mv.py

@@ -7,7 +7,7 @@
 from .modality_intent_join import episode_join
 
 @register_construct
-class EpisodeTreatmentMV(
+class TreatmentIntentMV(
     MaterializedViewMixin,
     Base,
 ):
@@ -21,13 +21,78 @@ class EpisodeTreatmentMV(
 
     mv_id: so.Mapped[int] = so.mapped_column(sa.Integer, primary_key=True)
 
+    treatment_episode_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    treatment_episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    treatment_episode_end_date: so.Mapped[date] = so.mapped_column(sa.Date)
+    treatment_episode_parent_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+
+    treatment_intent_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    treatment_intent_name: so.Mapped[str] = so.mapped_column(sa.String)
+
+    rt: so.Mapped[bool | None] = so.mapped_column(sa.Boolean)
+    sact: so.Mapped[bool | None] = so.mapped_column(sa.Boolean)
+    concurrent: so.Mapped[bool] = so.mapped_column(sa.Boolean)
+
+
+from .condition_episode_mv import ConditionEpisodeMV
+
+episode_summary_select = (
+    sa.select(
+        ConditionEpisodeMV.episode_id,
+        ConditionEpisodeMV.person_id,
+
+        ConditionEpisodeMV.episode_concept_id,
+        ConditionEpisodeMV.episode_label,
+
+        ConditionEpisodeMV.episode_start_date,
+        ConditionEpisodeMV.episode_end_date,
+
+        TreatmentIntentMV.treatment_episode_id,
+        TreatmentIntentMV.treatment_episode_start_date,
+        TreatmentIntentMV.treatment_episode_end_date,
+        TreatmentIntentMV.treatment_intent_concept_id,
+        TreatmentIntentMV.treatment_intent_name,
+
+        sa.func.coalesce(TreatmentIntentMV.rt, False).label("rt"),
+        sa.func.coalesce(TreatmentIntentMV.sact, False).label("sact"),
+        sa.func.coalesce(TreatmentIntentMV.concurrent, False).label("concurrent"),
+    )
+    .outerjoin(
+        TreatmentIntentMV,
+        TreatmentIntentMV.treatment_episode_parent_id
+        == ConditionEpisodeMV.episode_id
+    )
+)
+
+@register_construct
+class ConditionTreatmentIntentMV(
+    MaterializedViewMixin,
+    Base,
+):
+    __mv_name__ = "episode_treatment_mv"
+    __mv_select__ = episode_summary_select
+    __mv_index__ = "episode_id"
+    __deps__ = (ConditionEpisodeMV.__mv_name__, TreatmentIntentMV.__mv_name__)
+    __tablename__ = __mv_name__
+    __table_args__ = {"extend_existing": True}
+
+    mv_id: so.Mapped[int] = so.mapped_column(sa.Integer, primary_key=True)
+
     episode_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    person_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+
+    episode_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
+    episode_label: so.Mapped[str] = so.mapped_column(sa.String)
+
     episode_start_date: so.Mapped[date] = so.mapped_column(sa.Date)
     episode_end_date: so.Mapped[date] = so.mapped_column(sa.Date)
 
-    measurement_concept_id: so.Mapped[int] = so.mapped_column(sa.Integer)
-    concept_name: so.Mapped[str] = so.mapped_column(sa.String)
+    treatment_episode_id: so.Mapped[int | None] = so.mapped_column(sa.Integer, nullable=True)
+    treatment_episode_start_date: so.Mapped[date | None] = so.mapped_column(sa.Date, nullable=True)
+    treatment_episode_end_date: so.Mapped[date | None] = so.mapped_column(sa.Date, nullable=True)
+    treatment_intent_concept_id: so.Mapped[int | None] = so.mapped_column(sa.Integer, nullable=True)
+    treatment_intent_name: so.Mapped[str | None] = so.mapped_column(sa.String, nullable=True)
 
-    rt: so.Mapped[bool | None] = so.mapped_column(sa.Boolean)
-    sact: so.Mapped[bool | None] = so.mapped_column(sa.Boolean)
-    concurrent: so.Mapped[bool] = so.mapped_column(sa.Boolean)
+    rt: so.Mapped[bool | None] = so.mapped_column(sa.Boolean, nullable=True)
+    sact: so.Mapped[bool | None] = so.mapped_column(sa.Boolean, nullable=True)
+    concurrent: so.Mapped[bool | None] = so.mapped_column(sa.Boolean, nullable=True)